Constraint Based Modeling: FBA, FVA & Sampling — Hands-on

Learn how to turn genome scale metabolic models into quantitative prediction engines with constraint based modeling. This module covers FBA, FVA and sampling so that you can explore feasible flux spaces, growth predictions and intervention strategies in a reproducible way for systems biology and metabolic engineering projects.

Constraint Based Modeling: FBA, FVA & Sampling

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Session Index

Session 1 — FBA Formulation & Flux Space Basics Session 2 — Flux Variability Analysis & Alternative Optima Session 3 — Sampling, Robustness & Knockout Analysis Session 4 — Mini Capstone: End to End Constraint Based Workflow

Session 1

Fee: Rs 8800

FBA Formulation & Flux Space Basics

From stoichiometric matrix to linear program

S · v = 0 steady state constraint lower and upper bounds objective functions

Selecting objectives and media conditions

biomass maximisation uptake and secretion limits aerobic vs anaerobic cases

Toolchain for FBA on GEMs

COBRApy basics solvers (GLPK, CPLEX, Gurobi) loading SBML FBC models

Session 2

Fee: Rs 11800

Flux Variability Analysis & Alternative Optima

Why flux variability occurs in GEMs

underdetermined systems alternate optimal solutions network redundancy

Running FVA and interpreting ranges

min max fluxes for each reaction essential vs flexible reactions tightening bounds with data

Context specific constraints and phenotypes

tissue or condition specific bounds incorporating uptake and secretion data interpreting FVA results biologically

Session 3

Fee: Rs 14800

Sampling, Robustness & Knockout Analysis

Sampling feasible flux spaces

randomised sampling concepts hit and run style approaches distributions of reaction fluxes

Single and double gene or reaction knockouts

growth phenotype prediction synthetic lethality screens flux rerouting patterns

Robustness and sensitivity style analyses

parameter scans on bounds sensitivity of growth to nutrients interpreting robustness of phenotypes

Session 4

Fee: Rs 18800

Mini Capstone: End to End Constraint Based Workflow

Set up, run and interpret an FBA pipeline on a GEM

Theory + Practical

Combine FBA, FVA and knockouts for a case study

baseline growth and yields essential reactions and genes candidate engineering targets

Deliverables: notebooks, result tables and README

Jupyter or R notebooks CSV summaries of fluxes and phenotypes methods and parameter documentation

PDF

Constraint Based Modeling FBA FVA & Sampling Training | Flux Balance, Variability & Sampling

Constraint Based Modeling: FBA, FVA & Sampling — Hands-on